[Insight-users] ITK CUESTION
Angela
a.mendoza at alumnos.urjc.es
Mon Jun 20 11:44:15 EDT 2005
Thank. Are you know, How can I obtain images of itk (*.mha or mhd).
Where can I to find images itk for try.
Regards,
Angela
-----Mensaje original-----
De: insight-users-bounces+a.mendoza=alumnos.urjc.es at itk.org
[mailto:insight-users-bounces+a.mendoza=alumnos.urjc.es at itk.org] En nombre
de insight-users-request at itk.org
Enviado el: viernes, 17 de junio de 2005 13:50
Para: insight-users at itk.org
Asunto: Insight-users Digest, Vol 14, Issue 44
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Today's Topics:
1. any 3D nonrigid registration method in ITK? (Changhua Wu)
2. Re: FLTK+ITK, Getting Started IV, how to generate/config
myProjectGUI.fl? (Gavin Baker)
3. about level set (Yixun Liu)
4. about compiling of application based on ITK (Yixun Liu)
5. How can I get through InsightApplications-2.0.1 ???? (ºÆ ³Â)
6. RE: Re[3]: [Insight-users] about initial level set (Iv?n Mac?a)
7. calculate size of region in mm. (yasser salman)
8. Re: Re: How to Wrapper the ImageToHistogramGenerator Class
(Oliveira Marcelo)
----------------------------------------------------------------------
Message: 1
Date: Thu, 16 Jun 2005 18:07:11 -0700 (PDT)
From: Changhua Wu <wuchanghua at yahoo.com>
Subject: [Insight-users] any 3D nonrigid registration method in ITK?
To: insight-users at itk.org
Message-ID: <20050617010711.49493.qmail at web31504.mail.mud.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Hi,
I am looking for some 3D nonrigid registration
functions to registering two CT volumes of lung. Does
anyone know any registration method in ITK that can do
3D nonrigid registration. I tried demons. However, it
seems it can only process 2D images. Thanks.
Changhua Wu
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Message: 2
Date: Fri, 17 Jun 2005 11:49:54 +1000
From: Gavin Baker <gavinb+xtk at cs.mu.OZ.AU>
Subject: Re: [Insight-users] FLTK+ITK, Getting Started IV, how to
generate/config myProjectGUI.fl?
To: Xuelin Cui <xuelin at hawaii.edu>
Cc: ITK user <insight-users at itk.org>
Message-ID: <20050617014954.GB7382 at mundula.cs.mu.OZ.AU>
Content-Type: text/plain; charset=us-ascii
Hello Xuelin,
On Wed, Jun 15, 2005 at 09:44:18PM -1000, Xuelin Cui wrote:
> I am trying to test your example of "Getting Started IV", FLTK+ITK. But
> how to generate the source code of myProjectGUI.cxx? Also, how to sue
> fluid to generate the stuffs of myProjectGUI.fl?
Fluid is the FLTK interface builder, which is used to edit the .fl files
that describe the user interface. As well as editing the GUI in its WYSIWYG
mode, Fluid can generate the C++ implementation code from the .fl interface
description. This can be invoked from within Fluid using the File|Write
Code menu option, and also from the command line with the "-c" option.
However - if you use CMake and set up your project correctly, you don't have
to worry about that at all. CMake can automatically invoke Fluid for you,
and generate the GUI implementation code whenever the .fl changes. The
FLTK_WRAP_UI() command in CMake does this (provided you include the FLTK
package). Many of the ITK demo programs use ITK, so you can browse the
source and see how they did it.
The short version is, all you need to do in your CMakeLists.txt file is
include the FLTK package:
FIND_PACKAGE(FLTK)
IF(FLTK_FOUND)
INCLUDE_DIRECTORIES(${FLTK_INCLUDE_DIR})
ENDIF(FLTK_FOUND)
and then tell CMake to build the Fluid file for your application:
FLTK_WRAP_UI(myProject myProjectGUI.fl)
And that's all!
You can read more about FLTK and using Fluid at:
http://www.fltk.org
http://www.fltk.org/doc-1.1/fluid.html#FLUID
Andy has written a great CMake tutorial, available here:
http://www.linuxjournal.com/article/6700
:: Gavin
--
Gavin Baker Complex Systems Group
http://www.cs.mu.oz.au/~gavinb The University of Melbourne
------------------------------
Message: 3
Date: Fri, 17 Jun 2005 10:50:10 +0800
From: Yixun Liu <yxliu at fudan.edu.cn>
Subject: [Insight-users] about level set
To: insight-users at itk.org
Message-ID: <000a01c572e7$47b1e5a0$1f64a8c0 at YXLIU>
Content-Type: text/plain; charset="gb2312"
Hi,
I read the Level Set algorithm in ITKSofewareGuide. To generate a initial
Level set the general pipeline is that firstly smooth the image using a
edge-preserving smoother and then feed the relult as the input of the
GradientMagnitudeRecursiveGaussianImageFilter to get the gradient. I am very
confused. Because the GradientMagnitudeRecursiveGaussianImageFilter needs
smooth the image. This smooth will destroy the edge information which is
preserved by the edge-preserving filter.
Best regards,
Yixun LIu
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Message: 4
Date: Fri, 17 Jun 2005 11:23:37 +0800
From: Yixun Liu <yxliu at fudan.edu.cn>
Subject: [Insight-users] about compiling of application based on ITK
To: insight-users at itk.org
Message-ID: <001301c572eb$f366aa80$1f64a8c0 at YXLIU>
Content-Type: text/plain; charset="gb2312"
HI,
I always encounter the problem when I compile applicaton based on ITK. The
error is shown as below:
c:\program files\microsoft visual studio\vc98\include\ostream(354) : fatal
error C1076: compiler limit : internal heap limit reached; use /Zm to
specify a higher limit.
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------------------------------
Message: 5
Date: Fri, 17 Jun 2005 15:54:53 +0800
From: "ºÆ ³Â" <smhly at hotmail.com>
Subject: [Insight-users] How can I get through
InsightApplications-2.0.1 ????
To: Insight-users at itk.org
Message-ID: <BAY17-F101DC6EC9ADF16C8A23F4BACF40 at phx.gbl>
Content-Type: text/plain; format=flowed
plz help me ..
I use WinXP SP2
VC6.0
I have got VTK and InsightToolkit-2.0.1 well.
And set path well too.
compile information:
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡
¡¡¡¡¡¡
--------------------Configuration: BrainStripValidationApp - Win32
Release--------------------
Compiling...
BrainStripValidationApp.cxx
G:\Download\ITK\InsightToolkit-2.0.1\Code\BasicFilters\itkDanielssonDistance
MapImageFilter.txx(302)
: fatal error C1001: INTERNAL COMPILER ERROR
(compiler file 'E:\8168\vc98\p2\src\P2\main.c', line 494)
Please choose the Technical Support command on the Visual C++
Help menu, or open the Technical Support help file for more information
Error executing cl.exe.
ALL_BUILD - 1 error(s), 72 warning(s)
What can I do ?
I don't know what's wrong !
....
Chen Hao
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------------------------------
Message: 6
Date: Fri, 17 Jun 2005 09:57:15 +0200
From: Iv?n Mac?a <imacia at vicomtech.es>
Subject: RE: Re[3]: [Insight-users] about initial level set
To: "'Michal Postrozny'" <sandarak at wp.pl>, <luis.ibanez at kitware.com>,
<insight-users at itk.org>
Message-ID: <002901c57312$2ed7b020$2400a8c0 at vicomtech.es>
Content-Type: text/plain; charset="iso-8859-1"
Hi all,
The same thing happens to me with intensity 255 for the object and 0 for the
background. Is this the correct behaviour? In the software guide the
level-set function is positive inside and negative outside the zero
level-set. Shouldn't this be consistent with the fact that the foreground
(object) value is higher than the background value?
Thanks in advance
Ivan
> -----Mensaje original-----
> De: insight-users-bounces+imacia=vicomtech.es at itk.org
> [mailto:insight-users-bounces+imacia=vicomtech.es at itk.org] En
> nombre de Michal Postrozny
> Enviado el: jueves, 16 de junio de 2005 23:00
> Para: luis.ibanez at kitware.com; insight-users at itk.org
> Asunto: Re[3]: [Insight-users] about initial level set
>
>
> Hello Luis,
>
> After setting intensity of -1 for the segmented object
> (inside) and 1 for background (outside) everything works
> fine. Sorry for bothering you.
>
> Regards
>
> Michal Postrozny
>
> > Hello Luis,
>
> > You have said that there is no need to do anything with the binary
> > image, just feed it to the level set filter. I've tried to
> feed binary
> > image with intensities of 255 for segmented object and zero for
> > background to the GeodesicActiveContourLevelSetImageFilter.
> But this
> > doesn't work. I must be missing something important. After applying
> > ApproximateSignedDistanceMapImageFilter to the binary image and
> > feeding it to the geodesic everything works fine. But
> > ApproximateSignedDistanceMapImageFilter is rather slow, so
> if it was
> > possible to feed binary image directly to geodesic it would
> be great.
> > How can I achieve this?
>
> > Thanks in advance
>
> > Michal Postrozny
>
>
>
>
> >> Yixun,
>
>
> >> Don't need to do anything particular.
>
> >> You can feed your binary image directly as input level set.
>
>
> >> Regards,
>
>
> >> Luis
>
>
> >> ----------------
> >> Yixun Liu wrote:
>
> >>> Hi,
> >>>
> >>> I have a segmented image represented by binary image. I
> want to use
> >>> level set to refine the segmentation based on the
> segmented image.
> >>> How to generate a initial level set based on this binary image?
> >>>
> >>> Best regards,
> >>>
> >>> Yixun Liu
> >>>
> >>>
> >>>
> --------------------------------------------------------------------
> >>> ----
> >>>
> >>> _______________________________________________
> >>> Insight-users mailing list
> >>> Insight-users at itk.org
> >>> http://www.itk.org/mailman/listinfo/insight-users
>
>
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users
>
> --
> No virus found in this incoming message.
> Checked by AVG Anti-Virus.
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> 15/06/2005
>
>
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------------------------------
Message: 7
Date: Fri, 17 Jun 2005 04:48:52 -0700 (PDT)
From: yasser salman <yass71 at yahoo.com>
Subject: [Insight-users] calculate size of region in mm.
To: Luis Ibanez <luis.ibanez at kitware.com>
Cc: insight-users at itk.org
Message-ID: <20050617114852.75721.qmail at web50607.mail.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Hi luis..,
i'm using connectedthresholed image filter to segment
the tumor region
this is the part of calculating the no of pixels:
.
.
.
itk::RelabelComponentImageFilter<SegmentedImageType,SegmentedImageType>
RelabelImageFilter;
RelabelImageFilter::Pointer rcfilter=
RelabelImageFilter::New();
rcfilter->SetInput(connectedThreshold->GetOutput());
rcfilter->Update();
std::vector<unsigned long>::const_iterator it;
const std::vector<unsigned long> sizeOfObjects =
rcfilter->GetSizeOfObjectsInPixels();
it = sizeOfObjects.begin();
cout<<"No. of pixels ="<<*it<<"\n";
this code is working good but if i wanna to calculate
size of region in mm i changed "sizeOfObjects =
rcfilter->GetSizeOfObjectsInPixels();" TO
sizeOfObjects =
rcfilter->GetSizeOfObjectsInPhysicalUnits();
The following erroe occured:
"D:\InsightToolkit-1.6.0\Code\BasicFilters\
itkRelabelComponentImageFilter.h (129): error C2440:
'return' : cannot convert from 'const class
std::vector<float,class std::allocator<float> >' to
'const class std::vector<unsigned long,class
std::allocator<unsigned long> > &'Reason: cannot
convert from 'const class std::vector<float,class
std::allocator<float> >' to 'const class
std::vector<unsigned long,class
std::allocator<unsigned long> >'
No constructor could take the source type, or
constructor overload resolution was ambiguous
D:\InsightToolkit-1.6.0\Code\BasicFilters\itkRelabelComponentImageFilter.h(1
29)
: while compiling class-template member function
'const class std::vector<unsigned long,class
std::allocator<unsigned long> > &__thiscall
itk::RelabelComponentIm
ageFilter<class itk::Image<unsigned short,3>,class
itk::Image<unsigned short,3>
>::GetSizeOfObjectsInPhysicalUnits(void) const'
Error executing cl.exe."
should i change type def of the vector *it* or is
there any mismathing in the typedef i did it?
regard's
yasser
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Message: 8
Date: Fri, 17 Jun 2005 08:49:23 -0300 (ART)
From: Oliveira Marcelo <marceloitk at yahoo.com.br>
Subject: Re: [Insight-users] Re: How to Wrapper the
ImageToHistogramGenerator Class
To: Gaetan Lehmann <gaetan.lehmann at jouy.inra.fr>, Brad King
<brad.king at kitware.com>
Cc: insight-users at itk.org
Message-ID: <20050617114923.5191.qmail at web33204.mail.mud.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Hi Gaetan.
Tanxs a lot for your help. I think that wrapper
statistics package is a big problem for me and my
maybe the force isn't with me.
(http://www.itk.org/Wiki/ITK_Scripting).
please experts wrappers help me !!!! I need the
statical packages in my work and i love ITK.
[]'s
>
> Hi Brad,
> Hi Marcelo,
>
> There are several problem :
>
> + cable swig seems to have problem with
> itk::Statistics namespace
>
> Here is the error I get :
>
> Building object file
> wrap_itkImageToHistogramGeneratorPython.o...
>
/home/glehmann/itk/itk-mima2/build/Wrapping/CSwig/Numerics/wrap_itkImageToHi
stogramGeneratorPython.cxx:
>
> In function `PyObject*
>
_wrap_itkImageToHistogramGeneratorUS2_Pointer_GetPointer(PyObject*,
>
> PyObject*)':
>
/home/glehmann/itk/itk-mima2/build/Wrapping/CSwig/Numerics/wrap_itkImageToHi
stogramGeneratorPython.cxx:927:
>
> error: `itk::Statistics' has not been declared
> .....
>
> with the wrapper :
>
> #include "itkImage.h"
>
> #ifdef CABLE_CONFIGURATION
> #include "itkCSwigImages.h"
> #include "itkCSwigMacros.h"
> #include "itkScalarImageToHistogramGenerator.h"
>
> namespace _cable_
> {
> const char* const group =
> ITK_WRAP_GROUP(itkImageToHistogramGenerator);
> namespace wrappers
> {
> typedef
>
itk::Statistics::ScalarImageToHistogramGenerator<image::US2>::ScalarImageToH
istogramGenerator
>
> itkImageToHistogramGeneratorUS2;
> typedef
>
itk::Statistics::ScalarImageToHistogramGenerator<image::US2>::Pointer::Smart
Pointer
>
> itkImageToHistogramGeneratorUS2_Pointer;
> }
> }
> #endif
>
>
> Is there something to do to avoid this problem, Brad
> ?
>
>
> + ITK_WRAP_OBJECT1 can't be used for statistics, so
> you need to write your
> own macro (it's easy, look at itkCSwigMacros.h) or
> to write typedef by
> hand :-/
>
> + ImageToHistogramGenerator can't be used with
> image::F2
>
>
>
>
>
>
> On Tue, 14 Jun 2005 20:49:31 +0200, Oliveira Marcelo
>
> <marceloitk at yahoo.com.br> wrote:
>
> > Hi users and Gaetan,
> >
> > Gaetan will be a pleasure integrate my wrappers in
> > your branch
> > (http://voxel.jouy.inra.fr/darcs/itk-mima2). Tanx
> for
> > your wrappers.
> >
> > Ive been trying to wrapper the class
> > ImageToHistogramGenerator. Following the hints of
> > Gaetan and the
> http://www.itk.org/Wiki/ITK_Scripting
> >
> > i wrote the wrap_itkImageToHistogramGenerator.cxx
> > I dont know what i do with TImageType.
> >
> > #include "itkImage.h"
> > #include "itkImageToHistogramGenerator.h"
> >
> > #ifdef CABLE_CONFIGURATION
> > #include "itkCSwigMacros.h"
> > #include "itkCSwigImages.h"
> >
> > namespace _cable_
> > {
> > const char* const group =
> > ITK_WRAP_GROUP(itkImageToHistogramGenerator);
> > namespace wrappers
> > {
> > ITK_WRAP_OBJECT1(ImageToHistogramGenerator,
> > image::F2, itkImageToHistogramGeneratorF2);
> > ITK_WRAP_OBJECT1(ImageToHistogramGenerator,
> > image::F3, itkImageToHistogramGeneratorF3);
> > }
> > }
> >
> > #endif
> >
> >
> > And i got the errors:
> >
> >
>
local/oliveiramc/Doutorado/Insight_bin/Wrapping/CSwig/Numerics:
> > building default_target
> > Building wrap_itkImageToHistogramGenerator.xml
> from
> >
>
/local/oliveiramc/Doutorado/Insight_bin/Wrapping/CSwig/Numerics/wrap_itkImag
eToHistogramGenerator.xml...
> >
>
/local/oliveiramc/Doutorado/Insight/Wrapping/CSwig/Numerics/wrap_itkImageToH
istogramGenerator.cxx:31:
> > error: syntax
> > error before `::' token
> >
>
/local/oliveiramc/Doutorado/Insight/Wrapping/CSwig/Numerics/wrap_itkImageToH
istogramGenerator.cxx:31:
> > error: syntax
> > error before `::' token
> >
>
/local/oliveiramc/Doutorado/Insight/Wrapping/CSwig/Numerics/wrap_itkImageToH
istogramGenerator.cxx:32:
> > error: syntax
> > error before `::' token
> >
>
/local/oliveiramc/Doutorado/Insight/Wrapping/CSwig/Numerics/wrap_itkImageToH
istogramGenerator.cxx:32:
> > error: syntax
> > error before `::' token
> > make[5]: ***
> >
>
[/local/oliveiramc/Doutorado/Insight_bin/Wrapping/CSwig/Numerics/wrap_itkIma
geToHistogramGenerator.xml]
> > Error 1
> >
> >
> >
> >
> >
> >
> >
> >
> >
> ____________________________________________________
> > Yahoo! Mail, cada vez melhor: agora com 1GB de
> espaço grátis!
> > http://mail.yahoo.com.br
>
>
>
> --
> Gaetan Lehmann <gaetan.lehmann at jouy.inra.fr>
> Tel: +33 1 34 65 29 66
> Biologie du Développement et de la Reproduction
> INRA de Jouy-en-Josas (France)
> Web: http://voxel.jouy.inra.fr
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users
>
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